Hey Christopher,
Most of the components needed to have the editor modify the data files are there - reflection, serialization, asset/package browsing, and the inspect UI library. However it's not hooked up and last I heard, inspect needs to be modernized a bit. There have been a TON of improvements to reflect, but inspect has not kept pace beyond keeping it compiling. All the example json data files you see were created by hand.
The asset system doesn't depend on the renderer, bullet, etc. So you can safely remove any references to those systems in the json files. It should have no problem constructing just your components and you could build your own components to interact with whatever other libraries/middleware you choose.
A word about the state of the project in general: The good news is that the base systems are in really good shape. Reflect and the serialization layer support a broad range of data types. The asset/package system is a bit young and could use some cleanup, but the architecture is in place and it's not a huge chunk of code since reflect does 90% of the legwork. The work over the past few years has been towards laying a foundation that supports features usually reserved for AAA engines and that is scalable to large projects. Unfortunately, this has been at the expense of high-level features like the editor. So while there is a lot of work to do to make the engine usable by non-programmers, it could be a really solid foundation to build exactly what you want, and the data-driven asset/component system should give you a good way to pull in other libraries to fill in the gaps.
I'm really excited you're playing with helium and I know Geoff feels the same way. So we are definitely happy explain the architecture and offer suggestions for suiting it to your needs.
Philip